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Protein

Nigerythrin

Gene

ngr

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Exhibits NADH peroxidase activity (in vitro).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi40Iron 11
Metal bindingi73Iron 11
Metal bindingi73Iron 21
Metal bindingi115Iron 21
Metal bindingi118Iron 11
Metal bindingi149Iron 11
Metal bindingi149Iron 21
Metal bindingi152Iron 21
Metal bindingi174Iron 31
Metal bindingi177Iron 31
Metal bindingi189Iron 31
Metal bindingi192Iron 31

GO - Molecular functioni

Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Iron, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Nigerythrin
Gene namesi
Name:ngr
Ordered Locus Names:DVU_0019
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002194 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001350721 – 202NigerythrinAdd BLAST202

Proteomic databases

PaxDbiP30820.

Interactioni

Subunit structurei

Homodimer. May possess two rubredoxin-like centers and two hemerythrin-like binuclear-iron centers per dimer.

Protein-protein interaction databases

STRINGi882.DVU0019.

Structurei

Secondary structure

1202
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni10 – 12Combined sources3
Helixi29 – 56Combined sources28
Helixi60 – 87Combined sources28
Helixi104 – 120Combined sources17
Helixi122 – 133Combined sources12
Helixi136 – 161Combined sources26
Turni162 – 164Combined sources3
Beta strandi171 – 173Combined sources3
Beta strandi175 – 177Combined sources3
Beta strandi180 – 184Combined sources5
Turni190 – 192Combined sources3
Helixi196 – 198Combined sources3
Beta strandi200 – 202Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YUXX-ray1.60A/B1-202[»]
1YUZX-ray1.40A/B1-202[»]
1YV1X-ray1.50A/B1-202[»]
ProteinModelPortaliP30820.
SMRiP30820.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP30820.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini23 – 168Ferritin-like diironPROSITE-ProRule annotationAdd BLAST146
Domaini169 – 202Rubredoxin-likePROSITE-ProRule annotationAdd BLAST34

Sequence similaritiesi

Contains 1 ferritin-like diiron domain.PROSITE-ProRule annotation
Contains 1 rubredoxin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4108RAC. Bacteria.
COG1592. LUCA.
OMAiKVFLCPV.
OrthoDBiPOG091H01WH.
PhylomeDBiP30820.

Family and domain databases

CDDicd01041. Rubrerythrin. 1 hit.
Gene3Di1.20.1260.10. 1 hit.
2.20.28.10. 1 hit.
InterProiIPR009040. Ferritin-like_diiron.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR003251. Rubrerythrin.
[Graphical view]
PfamiPF02915. Rubrerythrin. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS50905. FERRITIN_LIKE. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P30820-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVRAQVPTV KNATNFNMVA DSKTAVGSTL ENLKAAIAGE TGAHAKYTAF
60 70 80 90 100
AKAAREQGYE QIARLFEATA AAELIHIGLE YALVAEMEPG YEKPTVAAPS
110 120 130 140 150
AYSCDLNLIS GANGEIYETS DMYPAFIRKA QEEGNSKAVH VFTRAKLAES
160 170 180 190 200
VHAERYLAAY NDIDAPDDDK FHLCPICGYI HKGEDFEKCP ICFRPKDTFT

AY
Length:202
Mass (Da):22,098
Last modified:May 24, 2004 - v3
Checksum:iDF5410519EE8D899
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti129K → E in AAC45480 (PubMed:9226272).Curated1
Sequence conflicti132E → G in AAC45480 (PubMed:9226272).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U71215 Genomic DNA. Translation: AAC45480.1.
AE017285 Genomic DNA. Translation: AAS94503.1.
RefSeqiWP_010937330.1. NC_002937.3.
YP_009244.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS94503; AAS94503; DVU_0019.
GeneIDi2794280.
KEGGidvu:DVU0019.
PATRICi32060008. VBIDesVul119526_0016.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U71215 Genomic DNA. Translation: AAC45480.1.
AE017285 Genomic DNA. Translation: AAS94503.1.
RefSeqiWP_010937330.1. NC_002937.3.
YP_009244.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YUXX-ray1.60A/B1-202[»]
1YUZX-ray1.40A/B1-202[»]
1YV1X-ray1.50A/B1-202[»]
ProteinModelPortaliP30820.
SMRiP30820.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi882.DVU0019.

Proteomic databases

PaxDbiP30820.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS94503; AAS94503; DVU_0019.
GeneIDi2794280.
KEGGidvu:DVU0019.
PATRICi32060008. VBIDesVul119526_0016.

Phylogenomic databases

eggNOGiENOG4108RAC. Bacteria.
COG1592. LUCA.
OMAiKVFLCPV.
OrthoDBiPOG091H01WH.
PhylomeDBiP30820.

Miscellaneous databases

EvolutionaryTraceiP30820.

Family and domain databases

CDDicd01041. Rubrerythrin. 1 hit.
Gene3Di1.20.1260.10. 1 hit.
2.20.28.10. 1 hit.
InterProiIPR009040. Ferritin-like_diiron.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR003251. Rubrerythrin.
[Graphical view]
PfamiPF02915. Rubrerythrin. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS50905. FERRITIN_LIKE. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNIGY_DESVH
AccessioniPrimary (citable) accession number: P30820
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: May 24, 2004
Last modified: November 30, 2016
This is version 113 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.